Molecular dynamics simulations of calcium-free calmodulin in solution

Journal of Biomolecular Structure & Dynamics
Cheng Yang, Krzysztof Kuczera

Abstract

A 4-ns molecular dynamics simulation of calcium-free calmodulin in solution has been performed, using Ewald summation to treat electrostatic interactions. Our simulation results were mostly consistent with solution experimental studies, including NMR, fluorescence and x-ray scattering. The secondary structures within the N- and C-terminal domains were conserved in the simulation, with trajectory structures similar to the NMR-derived model structure 1CFD. However, the relative orientations of the domains, for which there are no NMR restraints, differed in details between the simulation and the 1CFD model. The most interesting information provided by the simulations is that the dynamics of calcium-free calmodulin in solution is dominated by slow rigid body reorientations of the domains. The interdomain distance fluctuated between 29 and 39 A, and interdomain orientation angle, defined as the pseudo-dihedral formed by the four calcium binding sites, varied between -2 degrees and 108 degrees. Similarly, the domain linker region also exhibited significant fluctuations, with its length varying in the 34-45 A range and its bend angle in the 10-100 degrees range. The simulations are in accord with fluorescence results suggesting that c...Continue Reading

References

Dec 20, 1992·Journal of Molecular Biology·R ChattopadhyayaF A Quiocho
Aug 1, 1991·Protein Engineering·E L MehlerH Weinstein
Nov 5, 1988·Journal of Molecular Biology·Y S BabuW J Cook
Jun 5, 1988·Journal of Molecular Biology·D J Barlow, J M Thornton
Feb 14, 1971·Journal of Molecular Biology·B Lee, F M Richards
Sep 1, 1995·Nature Structural Biology·H KuboniwaA Bax
Jun 15, 1995·European Journal of Biochemistry·N TjandraA Bax
Jan 1, 1995·Annual Review of Biophysics and Biomolecular Structure·A Crivici, M Ikura
Aug 1, 1993·Protein Science : a Publication of the Protein Society·V BaudinC Poyart
Mar 1, 1993·Protein Science : a Publication of the Protein Society·S T RaoM Sundaralingam
Oct 1, 1996·Protein Science : a Publication of the Protein Society·D van der SpoelH J Vogel
Feb 1, 1996·Journal of Biomolecular Structure & Dynamics·A AmadeiH J Berendsen
Apr 17, 1998·Biophysical Journal·W WriggersK Schulten
Jul 20, 1999·Annual Review of Biophysics and Biomolecular Structure·C Sagui, T A Darden
Feb 2, 2000·Biophysical Journal·J García De La TorreB Carrasco
Apr 28, 2001·Biophysical Journal·D VigilA E García
Nov 8, 2001·Journal of Biomolecular Structure & Dynamics·C YangK Kuczera
Apr 30, 1998·The Journal of Physical Chemistry. B·A D MacKerellM Karplus

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Citations

Mar 17, 2004·Biochimica Et Biophysica Acta·Cheng YangKrzysztof Kuczera
Oct 2, 2002·Journal of Biomolecular Structure & Dynamics·Cheng Yang, Krzysztof Kuczera
Jan 29, 2008·Biophysical Journal·Gabriel GibratMarie-Claire Bellissent-Funel

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Methods Mentioned

BETA
FRET
X-ray

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